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Projects in Awesome Lists by stephaniehicks

A curated list of projects in awesome lists by stephaniehicks .

https://github.com/stephaniehicks/qsmooth

Smooth quantile normalization (qsmooth) is a generalization of quantile normalization, which is an average of the two types of assumptions about the data generation process: quantile normalization and quantile normalization between groups.

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/classroomnotes

Notes on academic-related things

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/methylcc

R/BioC package to estimate the cell composition of whole blood in DNA methylation samples in microarray or sequencing platforms

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/jhustatcomputing2022

Course website for Johns Hopkins BSPH Statistical Computing (Biostatistics 140.776) in Fall 2022

class computing statistics tidyverse

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/bioconductornotes

My notes/usage examples for various Bioconductor packages

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/jhustatprogramming2022

Course website for Biostat 840 in Fall 2022

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/spatialexperiment-analysis

repo to explore spatial data in R/Bioconductor and Python

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/scbatchpaper

Code used for the single-cell RNA-Seq batch effects paper

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/benchmark-hdf5-clustering

Benchmarking project for scalable clustering algorithms with large observations and HDF5 files

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/singlecellnano2017

Presentation at the Single Cell Nanocourse in Spring 2017 at Harvard Medical School

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/jhustatcomputing2021

Course website for JHSPH Statistical Computing (Biostatistics 140.776) in Fall 2021

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/quantro

quantro: Bioconductor package to test for global normalization assumptions

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/hansen-hicks-professional-development

Repository presentations and links to resources for professional development from joint lab meeting between Kasper Hansen (https://www.hansenlab.org) and Stephanie Hicks (https://www.stephaniehicks.com)

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/large-scale-data-base

Base Rmd files for Orchestrating Large-Scale Data Analysis in Bioconducotr

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/nihexploredata

Explores this data: https://exporter.nih.gov/ExPORTER_Catalog.aspx

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/jhuquantneuro2022

Course materials for the JHU Quantitative molecular neuroscience Fall 2022 course (ME.440.825.0001.FA22) from Stephanie Hicks

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/biocverse

project to create an interactive data viz of the biocoductor ecosystem

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/learnpython

A tutorial on learning the basics of programming in Python and performing data analysis in Python

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/atlasscalespatialclustering

Repo to share code for the atlas-scale spatial clustering CZI project

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/jhustatprogramming2023

Course website for Biostat 140.777 in Fall 2023

command-line data-science education github r-package r-programming sql

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/flowsorted.blood.wgbs.blueprint

A Bioconductor ExperimentHub data package for flow sorted purified whole blood cell types measured using DNA methylation on WGBS platform from BLUEPRINT

bioconductor bioconductor-package bisulfite-sequencing blood data dna-methylation flowsort wgbs

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/quantropaper

Additional material and scripts for the quantro manuscript

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/methylccpaper

This repository contains the additional material and scripts for the manuscript titled 'Technology-independent estimation of cell type composition using differentially methylated regions'

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/qsmoothpaper

This repository contains the additional material and scripts for the manuscript titled 'Smooth Quantile Normalization'

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/superwomen

Children's book titled Super Women: Growing Up to be Statisticians and Data Scientists

book childrens-books data-science statistics

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/scrna-kulkarni-macrophages

Project with Kulkarni lab to analyzing scRNA-seq macrophages in mouse

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/cshlcg2023

Course material from Stephanie Hicks for CSHL Computational Genomics 2023

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/quantrosim

This is the supporting data simulation package for the quantro R/Bioconductor package which can be used to simulate gene expression and DNA methylation data.

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/bodymaprat

This package contains a SummarizedExperiment object from the Yu et al. (2014) paper that performed the rat BodyMap across 11 organs and 4 developmental stages. PMID: 24510058

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/benchmarkfdrdata2019

Data and Benchmarking Results from Korthauer and Kimes et al. (2019)

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/fasthpluspaper

Files for the fasthplus paper

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/backgroundexperimentyeast

Gene expression experiment to measure NSB and optical noise in yeast

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/rafalabtips

Helpful tips for working in the Rafalab at DFCI/HSPH

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/postmut

Perl and R tool to combine functional predictions from SIFT, PolyPhen-2 and Xvar

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/robustpca

robust PCA exploration

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/new-course

Skeleton course website available to initialize future courses.

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/benchmark-kmeans

Repository to benchmark k-means using HDF5 files using (1) sci-kit learn in Python and (2) BiocSklearn in R/Bioconductor

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/trapnell2014myoblasthuman

This package contains a Bioconductor ExpressionSet from Trapnell et al. (2014) paper that performed a time-series experiment of bulk and single cell RNA-Seq at four time points in differentiated primary human myoblasts (GSE52529)

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/sc-dynamics-cml

single-cell dynamics in CML cancer patients

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/stephaniehicks

my personal repository

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/quantro-1

This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/quantro.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=quantro.

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/scrnaseqhumanmarinovsplitpool

Single cell and bulk RNA-Seq split/pool data from Marinov et al. (2014)

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/greetings

This is my greetings R package

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/projects_kulkarni

projects with Subhash Kulkarni at JHU School of Medicine

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/jhuads2021

Repo for JHU ADS 2021 lectures from Stephanie Hicks

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/mycaffydata

Gene expression of P493-6 cells expressing low or high levels of c-Myc. Data from Loven et al. (2012) Cell 151: 476-482.

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/datascience

Tools, Tips and Tricks for Data Science

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/introrandrstudio

Introduction to R, RStudio and the Tidyverse

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/hickslab_handbook

Onboarding for joining Stephanie Hicks's Lab at Johns Hopkins SPH

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/githubpages_tutorial

A tutorial on setting up websites with GitHub Pages using jekyll

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/biostat776-intro-stephanie-hicks

Website for Stephanie Hicks in Biostatistics 776

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/cshlcg2022

Course material from Stephanie Hicks for CSHL Computational Genomics 2022 course

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/website-hicks-source

source for academic website

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/cshlgsd2022

Course material from Stephanie Hicks for CSHL Genome Scale Data 2022

Last synced: 11 Nov 2024

https://github.com/stephaniehicks/topsecret

shhhhh

Last synced: 11 Nov 2024